Why are the deformation bones offsets from the Meta-rig after generating?
Seeing a similar sounding issue, I noticed that the meta-rig set up before generating had a translation that suspiciously matched the offset of the deformation bones seen afterwards (seen from the Transform->Location: in the properties panel)

If I first made sure to apply any transforms to the meta-rig before generating (Ctrl-A) that removed the offset. Maybe some un-applied meta-rig transform is the cause of the offset for you too.